Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[WIP] Add retip tool suit wrapper(s) #3

Closed
wants to merge 30 commits into from
Closed

[WIP] Add retip tool suit wrapper(s) #3

wants to merge 30 commits into from

Commits on Sep 7, 2020

  1. Add retip tool suit wrapper(s) for deployment into TTS.

    @smartx-usman
    smartx-usman committed Sep 7, 2020
    Configuration menu
    Copy the full SHA
    da5b70f View commit details
    Browse the repository at this point in the history

Commits on Sep 17, 2020

  1. add aplcms

    @xtracko @martenson
    xtracko authored and martenson committed Sep 17, 2020
    Configuration menu
    Copy the full SHA
    73a5b87 View commit details
    Browse the repository at this point in the history

  2. switch to public image

    @martenson
    martenson committed Sep 17, 2020
    Configuration menu
    Copy the full SHA
    890ce18 View commit details
    Browse the repository at this point in the history

Commits on Sep 18, 2020

  1. add xmsannotator

    @xtracko @martenson
    xtracko authored and martenson committed Sep 18, 2020
    Configuration menu
    Copy the full SHA
    5a9decb View commit details
    Browse the repository at this point in the history

  2. adjust tool version so it corresponds to the downstream software

    @martenson
    martenson committed Sep 18, 2020
    Configuration menu
    Copy the full SHA
    93745d1 View commit details
    Browse the repository at this point in the history

Commits on Sep 21, 2020

  1. Changed galaxy xml file to use conda biotransformer package

    @trachtok
    trachtok committed Sep 21, 2020
    Configuration menu
    Copy the full SHA
    53bd11c View commit details
    Browse the repository at this point in the history

Commits on Sep 22, 2020

  1. update versioning to iuc standard 

    add missing requirement
drop extra whitespace
    @martenson
    martenson committed Sep 22, 2020
    Configuration menu
    Copy the full SHA
    0d0df54 View commit details
    Browse the repository at this point in the history

  2. Changed galaxy xml file to use conda biotransformer package

    @trachtok @smartx-usman
    trachtok authored and smartx-usman committed Sep 22, 2020
    Configuration menu
    Copy the full SHA
    459f828 View commit details
    Browse the repository at this point in the history

  3. Use proper versioning semantics. Add basic tests and associated files… 

    …. Modify datatype to use more generic type rather than custom defined type. Use docker image from DockerHub.
    @smartx-usman
    smartx-usman committed Sep 22, 2020
    Configuration menu
    Copy the full SHA
    0771801 View commit details
    Browse the repository at this point in the history

  4. Correction of flake8 errors in Python wrapper

    @trachtok
    trachtok committed Sep 22, 2020
    Configuration menu
    Copy the full SHA
    feeab17 View commit details
    Browse the repository at this point in the history

  5. lint omport order

    @martenson
    martenson committed Sep 22, 2020
    Configuration menu
    Copy the full SHA
    c6918a6 View commit details
    Browse the repository at this point in the history

  6. Merge pull request #7 from RECETOX/biot_up 

    update biotransformer versioning to iuc standard
    @martenson
    martenson committed Sep 22, 2020
    Configuration menu
    Copy the full SHA
    8338173 View commit details
    Browse the repository at this point in the history

Commits on Sep 23, 2020

  1. Remove the unnecesarry data tables

    Jiří Novotný committed Sep 23, 2020
    Configuration menu
    Copy the full SHA
    53a1a67 View commit details
    Browse the repository at this point in the history

  2. Populate help section and adapt wrappers to the package API changes

    Jiří Novotný committed Sep 23, 2020
    Configuration menu
    Copy the full SHA
    d5516ef View commit details
    Browse the repository at this point in the history

  3. Merge pull request #6 from RECETOX/xmsannotator 

    [WIP] add xmsannotator
    @xtracko
    xtracko committed Sep 23, 2020
    Configuration menu
    Copy the full SHA
    9c62378 View commit details
    Browse the repository at this point in the history

  4. Migrate towards HDF5 outputs

    Jiří Novotný committed Sep 23, 2020
    Configuration menu
    Copy the full SHA
    3ab532b View commit details
    Browse the repository at this point in the history

Commits on Sep 24, 2020

  1. Merge pull request #5 from RECETOX/aplcms 

    [WIP] add apLCMS
    @xtracko
    xtracko committed Sep 24, 2020
    Configuration menu
    Copy the full SHA
    5305d1a View commit details
    Browse the repository at this point in the history

  2. Change error detection policy 

    Error in stderr is actually correct behavior.
    Jiří Novotný committed Sep 24, 2020
    Configuration menu
    Copy the full SHA
    f4d7aa1 View commit details
    Browse the repository at this point in the history

  3. Fix requerement

    Jiří Novotný committed Sep 24, 2020
    Configuration menu
    Copy the full SHA
    277cb8e View commit details
    Browse the repository at this point in the history

  4. Merge pull request #9 from RECETOX/aplcms 

    Adapt apLCMS to HDF5 files
    @xtracko
    xtracko committed Sep 24, 2020
    Configuration menu
    Copy the full SHA
    b6bca87 View commit details
    Browse the repository at this point in the history

  5. Merge pull request #10 from RECETOX/xmsannotator 

    Change xmsannotator error detection policy
    @xtracko
    xtracko committed Sep 24, 2020
    Configuration menu
    Copy the full SHA
    f92295d View commit details
    Browse the repository at this point in the history

  6. Cleaned xml wrapper and added test.

    @trachtok
    trachtok committed Sep 24, 2020
    Configuration menu
    Copy the full SHA
    ef7d82e View commit details
    Browse the repository at this point in the history

  7. Repaired broken xml tags

    @trachtok
    trachtok committed Sep 24, 2020
    Configuration menu
    Copy the full SHA
    c98db22 View commit details
    Browse the repository at this point in the history

Commits on Sep 25, 2020

  1. More cleaning of xml wrapper.

    @trachtok
    trachtok committed Sep 25, 2020
    Configuration menu
    Copy the full SHA
    4ce18f4 View commit details
    Browse the repository at this point in the history

  2. Merge pull request #12 from RECETOX/biot_up 

    Cleaned xml wrapper and added test.
    @martenson
    martenson committed Sep 25, 2020
    Configuration menu
    Copy the full SHA
    9465281 View commit details
    Browse the repository at this point in the history

Commits on Sep 29, 2020

  1. Add retip tool suit wrapper(s) for deployment into TTS.

    @smartx-usman
    smartx-usman committed Sep 29, 2020
    Configuration menu
    Copy the full SHA
    bcd9f6f View commit details
    Browse the repository at this point in the history

  2. Use proper versioning semantics. Add basic tests and associated files… 

    …. Modify datatype to use more generic type rather than custom defined type. Use docker image from DockerHub.
    @smartx-usman
    smartx-usman committed Sep 29, 2020
    Configuration menu
    Copy the full SHA
    d30d338 View commit details
    Browse the repository at this point in the history

  3. Fix tool version.

    @smartx-usman
    smartx-usman committed Sep 29, 2020
    Configuration menu
    Copy the full SHA
    0532b80 View commit details
    Browse the repository at this point in the history

  4. Remove lines diff for binary files.

    @smartx-usman
    smartx-usman committed Sep 29, 2020
    Configuration menu
    Copy the full SHA
    11db27e View commit details
    Browse the repository at this point in the history

  5. Merge remote-tracking branch 'origin/master' 

    # Conflicts:
#	tools/biotransformer/biotransformer.xml
#	tools/biotransformer/wrapper_biotransformer.py
#	tools/retip/macros.xml
#	tools/retip/retip_apply.xml
#	tools/retip/retip_descriptors.xml
    @smartx-usman
    smartx-usman committed Sep 29, 2020
    Configuration menu
    Copy the full SHA
    171af41 View commit details
    Browse the repository at this point in the history